RNA sequencing of 4N intestinal and non-intestinal C. elegans cells in L1

Endomitosis is a non-canonical cell cycle in which cells undergo all four phases of a canonical cell cycle (G1, S, G2 and M), but do not initiate or complete cytokinesis during M phase. To identify the transcriptional differences between endomitosis and canonical cell cycles in C. elegans, we isolated cells from L1 larvae of a strain expressing intestinal-specific mCherry (elt-2p::mCherry-PH-P2A-H2B-mCherry) grown for 6 hours at 20ºC. We sorted intestinal and non-intestinal cells both with a 4N DNA content by FACS based on the mCherry expression and the Hoechst-34580 profile. We performed RNA-seq in intestinal (3 replicates) and non-intestinal cells (3 replicates) and differential gene expression analysis to identify the genes that are upregulated or downregulated in intestinal endomitosis compared to canonical cell cycles. mRNA profiles of intestinal (3 biological replicates) and non-intestinal cells (3 biological replicates) generated from pools of 500 cells with an adapted CEL-seq protocol and paired-end sequencingon an Illumina NextSeq500 platform.